Genomic Sequencing for Clinical Care - Genome.gov · Genome Sequencing for Clinical Care Dan M....
Transcript of Genomic Sequencing for Clinical Care - Genome.gov · Genome Sequencing for Clinical Care Dan M....
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Future Opportunities for Genome Sequencing
Genome Sequencing for Clinical Care
Dan M. Roden, MD
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Green and Guyer,. 2011
• Genomic predictors of disease susceptibility and drug response • Engaging the Electronic Medical Record (EMR)
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Implementing genomic medicine
Green and Guyer,. 2011
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Clinical Center Genomics
Opportunity
NSIGHT
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Demonstration projects to incorporate genomic information into EMRs with decision support
• family history • hypertension management in AAs • Pharmacogenetic variant implementation • Diabetes diagnosis: Sequencing ~40 diabetes/
lipodystrophy/obesity genes in targeted patients
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Clinical Center Genomics
Opportunity
• ~1000 exomes: projects 50-300 exomes each
• Evidence for Mendelian, single gene etiology • Actual NIHCC patients • Germline prioritized over somatic
sequencing • Consent & protocol language in place • Sequencing at NIH intramural center;
“CLIA valid” • PI designates staff for analysis of
primary variants; returns primary findings
• NHGRI analyzes & returns secondary findings
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• >350,000 subjects with DNA samples + EMRs across 10 sites
• electronic phenotyping; GWAS genotyping • phenotype genotype • genotype phenotype (“PheWAS”)
• eMERGE-PGx: Targeted sequencing across pharmacogenes
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eMERGE-PGx Pharmacogene sequencing project • identify patients • identify “actionable” variants • sequence
implement actionable
variants
create a repository of all
variants
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A variant of unknown significance problem
Of the first 2,022 eMERGE-PGx subjects • 128 non-synonymous variants in SCN5A
and KCNH2 • 121/127 MAF <0.5%; 92 singletons • 3 expert annotators asked to assign
pathogenicity
congenital long QT syndromes caused by mutations in ion channel genes, including SCN5A and KCNH2
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Lab 1 16/121
Lab 2 24/121
Lab 3 17/121
4
EMR review (n=48): • 1 with atrial fibrillation • 31/48 with ECGs: 1/31 with long QT Issues: • return which results? which (if any) patients to have
ECGs? screen families? which? what if new data changes the interpretation?
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ClinGen The Clinical Genome Resource
Launched Sept 2013
NCBI ClinVar Leads Melissa Landrum Donna Maglott
Steve Sherry
U41 Grant PIs David Ledbetter Christa Martin Bob Nussbaum
Heidi Rehm
U01 PIs Jonathan Berg
Jim Evans David Ledbetter
Mike Watson
U01 PIs Carlos Bustamante
Sharon Plon
NHGRI/NICHD/NCI Program Directors
Erin Ramos Lisa Brooks
Danuta Krotoski Sheri Schully
• ClinVar is a database developed and maintained by NCBI with input from the community, including ClinGen investigators
• ClinGen, The Clinical Genome Resource: •Standardizing, sharing, and developing new methods for annotation, interpretation, and assessment of actionability of genomic variants
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• 3,500 patients, 10 projects • Individualized phenotypes
genotype • Standardized exome/genome
sequencing and reporting • Ongoing ELSI assessments
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• Healthy individuals • Preconception carrier screening • Cardiomyopathy • Childhood cancers • Adult cancers • Susceptibility to colon cancer and polyps • Intellectual disabilities • Hearing loss
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Major questions
• Patient characteristics that signal potential utility of whole genome or exome sequencing
• How to analyze large data sets in a clinical environment
• Special considerations in different populations
• Management of “non-target” data
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The numbers As of March 2014: • 1,532 subjects; 69% adult; 52% female
• White 74% • African American 7% • Hispanic 8% • Asian 3% • American Indian 2% • Not Reported 7%
• Total Sequenced: 1049 • 232 Tumor-focused • 817 Germline-focused
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The numbers Germline analysis (n=817) • “Positive” for diagnostic finding: 241 (29%) • Incidental Findings per ACMG list: 24 (2.9%)
• Incidental Findings by relaxed criteria: 46 (5.6%)
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Cases (+) Possible (-) Yield
Cancer (Pediatric) 115 11 10 94 18% Cancer (Adult) 109 9 25 75 31% Dysmorphology 41 10 7 24 41% Heart Disease 48 10 11 27 44% Bilateral sensorineural hearing loss 24 3 8 13 46% Neurological Diagnosis 108 24 27 57 47% Retinal 41 8 13 20 51% Preconception (Carrier) 7 5 0 2 71%
Diagnostic yield by initial diagnosis (Germline analyses)
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Pediatric Solid Tumor exome results Highest category somatic mutation found per patient (n=81)
Only somatic mutations in
“non-cancer genes”
Mutations of “potential clinical utility”
Mutations in other known “cancer genes”
Mutations of “established clinical utility” in that tumor type
Category 1 (2%)
Category 3 (23%)
Category 2 (26%) Category 4 (49%)
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• Informed consent : • analysis across sites • formulation of specific recommendations for best practices • Factors influencing patient understanding & outcomes
• Incidental Findings • Frequency of “medically actionable” incidental findings: 3-6% • CSER sites input into ongoing ACMG policy formulation on
return of results • Accruing data on what patients wish to know
• Collecting data on measures of patient satisfaction/distress with regard to both diagnostic findings and off-target results
A major focus on ELSI from the onset
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Going forward Assessing the impact of sequencing findings across time and families: • Of the patients with incidental findings, how
many had clinical work-ups for the condition • Of these patients how often were there
phenotypic features of the genotype described. • Derive initial cost-effectiveness assessments of
the reporting of incidental findings. • How are findings transmitted to family
members • Issues of re-interpretation of genomic data after
the initial report
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Clinical Center Genomics
Opportunity
Common issues • EMR integration • Return of results • Actionability: target and incidental • Data sharing concerns • Longitudinal issues: what happens to patients over
time? What happens when interpretation changes over time?
NSIGHT Undiagnosed disease network
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Genomic Medicine working group: meeting 6
Opportunities for international
collaborations
50 participants 25 countries
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Genomic Medicine working group: meeting 6
Opportunities for international
collaborations • Evidence generation • Health information technology • Education/workforce development: Genomics
professionals; bioinformatics expertise ; Other health professionals; Public
• Pharmacogenomics • Policy: Data sharing and regulatory issues; Costs and
benefits
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Widely Available Clinical Capability
Today (%) Desired in 3-5
Years (%) Pharmacogenomics 11 56
Germline Sequencing 11 17
Tumor Sequencing 11 29
Rare Disease Diagnosis 6 17
Microbial Pathogen Identification 11 53
Systematic Family History 46 71
Genetic Counselors 30 77
Electronic Medical Record 30 94
Clinical Decision Support 33 94
GM6: Clinical capabilities today and desired
< 33% 34-66% > 66%
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What are the challenges? -1
351,000
200,000
500,000
500,000
250,000
52,000200,000
5,600,000 300,000
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What are the challenges? -2 • Quality of data and analysis: what is the
indication? Whole genome versus targeted. Beyond SNVs. identifying and using modifier variants
• What is an actionable variant? for the indication; incidental findings
• Understanding and interpreting variants • Engaging patients: satisfaction, expectations,
incidental findings. Privacy; consent • Potential for poor and costly care if
sequencing introduced inappropriately
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What are the challenges? -3 • outcomes (including cost effectiveness) • diverse ancestries • training • expand scope to non-academic clinical settings • implementation and integration in EMR
environments • mechanics of information generation and delivery;
e.g. interacting with CAP • need for large datasets linking genotypes and
phenotypes • Interfacing with regulators (e.g. FDA) and payers
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If NHGRI doesn’t take coordinated action, the promise of genomic medicine will be delayed
NHGRI imperatives – maximize benefit/minimize risk
• which patients, which targets. • analysis of genomes for discovery and implementation • accrual of Large genotype-phenotype datasets across
ancestries to understand variant function • work out the realities of implementation: consenting,
EHR integration, patient and provider education, clinical decision support, follow-up…
• promoting analysis of economic and health outcomes